Variant

Genome Chromosome Position VCF ID Ref Alt mRNA Change mRNA Info
GRCh37 chr4 103789885 . T A CCDS3659.1:NM_181893.2:c.17aAg>aTg_NP_871622.1:p.6K>M Homo sapiens ubiquitin conjugating enzyme E2 D3 (UBE2D3), transcript variant 9, mRNA.
pdb_id
label_asym_id
label_seq_id
label_comp_id
auth_asym_id
auth_seq_id
alphafold_id
label_asym_id
label_seq_id
label_comp_id
auth_asym_id
auth_seq_id

PDB

Entity Residue Monomer BioUnit Ligand View
PDB Entity Uniprot Identity Evalue ExpMethod Date Name Label Auth ASA rASA SS φ ψ ASA rASA ΔASA Interaction Name Distance Atom(p) Atom(l)
3l1z 1 P61077 97.92 1e-104 X-RAY
2010-05-05 LYS A:14 A:4 161.0 0.805 H -51.6 -40.0 104.0 0.52 0.285 B:O95155:0.285
HOH
9.923
N
O
4s3o 1 P61077 96.6 1e-104 X-RAY
2015-07-15 LYS A:5 A:4 42.0 NA H -58.4 -44.4 NA NA NA
LYS B:5 D:4 145.0 0.725 H -59.2 -45.3 126.0 0.63 0.095 D:Q99496:0.095
ZN
HOH
8.787
2.626
NZ
O
ZN
O
3rpg 1 P61077 96.6 1e-104 X-RAY
2011-08-17 LYS A:6 A:4 133.0 0.665 H -66.4 -49.8 114.0 0.57 0.095 C:Q99496:0.095
ZN
HOH
8.482
3.783
NZ
CB
ZN
O
5ifr 1 P61077 96.6 2e-104 X-RAY
2016-05-11 LYS A:8 A:4 150.0 0.75 H -76.2 -26.5 150.0 0.75 0.0 HOH
7.018
CG
O
5egg 1 P61077 97.92 2e-104 X-RAY
2016-11-02 LYS A:13 A:4 125.0 0.625 H -70.3 -38.5 125.0 0.625 0.0 HOH
5.652
O
O
1x23 1 P61077 97.92 2e-104 X-RAY
2005-05-03 LYS A:12 A:4 138.0 0.69 H -56.8 -47.5 138.0 0.69 0.0 HOH
2.594
O
O
LYS B:12 B:4 143.0 0.715 H -58.6 -43.5 NA NA NA
LYS C:12 C:4 128.0 0.64 H -70.0 -35.9 NA NA NA
LYS D:12 D:4 119.0 0.595 H -56.5 -44.6 NA NA NA
7lyb 7 P61077 97.92 3e-104 EM
2021-07-28 LYS J:22 P:4 92.0 0.46 H -66.5 -33.8 92.0 0.46 0.0
4r8p 8 Q99496,P61077 96.6 6e-104 X-RAY
2014-11-05 LYS L:125 L:204 93.0 0.465 H -63.3 -41.7 93.0 0.465 0.0
LYS N:125 N:204 45.0 NA H -60.7 -39.3 45.0 NA NA
6cp0 2 P61077 97.22 1e-103 X-RAY
2018-08-01 LYS B:6 B:4 168.0 0.84 H -85.9 -39.2 55.0 0.275 0.565 A:Q6RCR3:0.565
3ugb 1 P61077 97.22 1e-103 X-RAY
2012-05-16 LYS A:4 A:4 186.0 0.93 H -63.6 -41.1 186.0 0.93 0.0 HOH
3.183
O
O
4bvu 2 P61077 97.22 1e-103 X-RAY
2014-01-29 LYS B:4 B:4 192.0 0.96 H -54.3 -43.1 133.0 0.665 0.295 A:Q99PZ6:0.295
HOH
3.424
CB
O
7bol 1 P62837 95.83 4e-103 X-RAY
2021-03-24 LYS A:5 A:4 132.0 0.66 H -67.4 -40.5 132.0 0.66 0.0 HOH
2.534
HE3
O
2esk 1 P62837 95.83 4e-103 X-RAY
2005-12-06 LYS A:6 A:4 138.0 0.69 H -61.8 -42.9 138.0 0.69 0.0 HOH
2.496
NZ
O
3tgd 1 P62837 95.83 4e-103 X-RAY
2011-08-31 LYS A:9 A:4 119.0 0.595 H -62.3 -40.2 119.0 0.595 0.0 HOH
2.785
O
O
1w4u 1 P51669 95.83 4e-103 NMR
2004-11-10 LYS A:4 A:4 98.0 0.49 H -85.0 -16.2 98.0 0.49 0.0
4a49 2 P62837 95.83 4e-103 X-RAY
2012-01-25 LYS B:4 B:4 161.0 0.805 H -67.2 -36.8 81.0 0.405 0.4 A:P22681:0.4
ZN
K
HOH
9.079
7.090
2.719
CB
O
O
ZN
K
O
4a4b 3 P62837 95.83 4e-103 X-RAY
2012-01-25 LYS C:4 C:4 85.0 NA H -54.4 -30.4 41.0 NA NA A:P22681:NA
ZN
9.745
CB
ZN
4a4c 3 P62837 95.83 4e-103 X-RAY
2012-01-25 LYS C:4 C:4 180.0 0.9 H -55.0 -40.9 111.0 0.555 0.345 A:P22681:0.345
ZN
9.134
CB
ZN
5d1k 1 P62837 95.83 4e-103 X-RAY
2015-10-28 LYS A:4 A:4 186.0 0.93 H -64.0 -42.3 75.0 0.375 0.555 B:Q96BH1:0.555
ZN
HOH
9.861
2.884
CB
O
ZN
O
5d1l 1 P62837 95.83 4e-103 X-RAY
2015-10-28 LYS A:4 A:4 187.0 0.935 H -60.8 -42.1 73.0 0.365 0.57 B:Q96BH1:0.57
ZN
HOH
9.984
2.966
CB
O
ZN
O
5d1m 1 P62837 95.83 4e-103 X-RAY
2015-10-28 LYS A:4 A:4 190.0 0.95 H -61.7 -41.0 79.0 0.395 0.555 B:Q96BH1:0.555
ZN
HOH
9.885
2.921
CB
N
ZN
O
3eb6 2 P62840 95.83 5e-103 X-RAY
2008-09-09 LYS B:6 B:4 124.0 0.62 H -53.3 -31.7 64.0 0.32 0.3 A:Q13489:0.3
ZN
6.996
NZ
ZN
6m2c 1 P62837 95.83 5e-103 X-RAY
2021-04-07 LYS A:6 A:4 120.0 0.6 H -67.4 -36.9 119.0 0.595 0.005 E:Q969V5:0.005
ZN
HOH
9.063
9.401
HD2
O
ZN
O
LYS B:6 B:4 164.0 0.82 H -69.3 -38.8 NA NA NA
LYS C:6 C:4 161.0 0.805 H -69.3 -38.5 NA NA NA
LYS D:6 D:4 153.0 0.765 H -65.3 -42.5 NA NA NA
2clw 1 P62837 95.83 7e-103 X-RAY
2007-06-12 LYS A:22 A:4 117.0 0.585 H -68.5 -36.0 117.0 0.585 0.0 HOH
2.822
CD
O
2clw 2 P62837 95.83 7e-103 X-RAY
2007-06-12 LYS B:22 B:4 129.0 0.645 H -73.0 -33.4 NA NA NA
LYS C:22 C:4 144.0 0.72 H -65.1 -31.5 NA NA NA
LYS D:22 D:4 122.0 0.61 H -67.1 -33.9 NA NA NA
3l1y 1 P62837 95.14 1e-102 X-RAY
2010-05-05 LYS A:14 A:4 107.0 0.535 H -63.6 -42.1 107.0 0.535 0.0 HOH
2.696
O
O
2esq 1 P62837 95.14 2e-102 X-RAY
2005-12-06 LYS A:6 A:4 143.0 0.715 H -59.3 -44.6 143.0 0.715 0.0 HOH
2.844
O
O
7jzv 1 A0A386IN42,P61077 97.22 2e-102 EM
2021-02-17 LYS A:115 A:204 54.0 0.27 H -56.6 -39.6 54.0 0.27 0.0
2eso 1 P62837 95.14 2e-102 X-RAY
2005-12-06 LYS A:6 A:4 124.0 0.62 H -64.7 -40.1 124.0 0.62 0.0 HOH
2.843
O
O
2esp 1 P62837 95.14 2e-102 X-RAY
2005-12-06 LYS A:6 A:4 126.0 0.63 H -62.1 -45.0 126.0 0.63 0.0 CL
HOH
3.831
2.749
CE
O
CL
O
3a33 1 P62837 95.14 4e-102 X-RAY
2009-11-24 LYS A:7 A:4 158.0 0.79 H -58.6 -41.9 158.0 0.79 0.0 HOH
7.529
N
O
4ddg 1 P62837,Q96FW1 95.14 5e-102 X-RAY
2012-02-22 LYS A:6 A:4 146.0 0.73 H -52.6 -47.2 144.0 0.72 0.01 C:P62837+Q96FW1:0.01
LYS B:6 B:4 143.0 0.715 H -52.6 -47.2 143.0 0.715 0.0
LYS C:6 C:4 147.0 0.735 H -52.5 -47.2 147.0 0.735 0.0
LYS J:6 J:4 147.0 0.735 H -52.6 -47.3 NA NA NA
LYS K:6 K:4 144.0 0.72 H -52.5 -47.2 NA NA NA
LYS L:6 L:4 147.0 0.735 H -52.7 -47.3 NA NA NA
4ddi 1 P62837,Q96FW1 95.14 5e-102 X-RAY
2012-02-22 LYS A:6 A:4 151.0 0.755 H -61.6 -37.5 151.0 0.755 0.0
LYS B:6 B:4 152.0 0.76 H -61.6 -37.5 151.0 0.755 0.005 A:P62837+Q96FW1:0.005
LYS C:6 C:4 150.0 0.75 H -61.7 -37.4 149.0 0.745 0.005 B:P62837+Q96FW1:0.005
4ldt 3 P62837 95.14 6e-102 X-RAY
2013-08-14 LYS C:5 C:4 127.0 0.635 H -61.1 -42.7 125.0 0.625 0.01 A:Q96FW1+Q9XVR6:0.01
HOH
2.717
O
O
4wz3 1 P62837 95.14 6e-102 X-RAY
2015-01-07 LYS A:5 A:4 157.0 0.785 H -57.9 -47.3 103.0 0.515 0.27 B:Q5X159:0.27
HOH
3.631
CE
O
6hpr 3 P62837 95.14 1e-101 X-RAY
2018-12-12 LYS C:4 C:4 82.0 NA H -61.4 -42.7 58.0 NA NA A:Q13490:NA
HOH
3.045
N
O
4v3l 1 P62837 95.14 1e-101 X-RAY
2015-04-08 LYS A:3 A:4 182.0 0.91 H -61.2 -42.6 182.0 0.91 0.0 HOH
2.764
O
O
5zbu 1 P62837 95.14 1e-101 X-RAY
2019-02-27 LYS A:5 C:4 148.0 0.74 H -59.3 -50.4 96.0 0.48 0.26 D:O43567:0.26
ZN
7.063
NZ
ZN
LYS B:5 B:4 160.0 0.8 H -60.4 -48.9 NA NA NA
3jvz 1 P62837 94.44 3e-101 X-RAY
2010-01-12 LYS A:3 A:4 180.0 0.9 H -55.7 -34.1 93.0 0.465 0.435 C:Q96PU5:0.435
LYS B:3 B:4 166.0 0.83 H -47.6 -45.9 NA NA NA
3jw0 1 P62837 94.44 3e-101 X-RAY
2010-01-12 LYS A:3 A:4 181.0 0.905 H -49.5 -36.9 90.0 0.45 0.455 C:Q96PU5:0.455
LYS B:3 B:4 154.0 0.77 H -77.9 -42.7 NA NA NA
5mnj 1 P62837 94.44 5e-101 X-RAY
2017-05-31 LYS A:4 A:4 83.0 NA H -57.0 -42.0 54.0 NA NA C:Q00987:NA
ZN
9.597
CB
ZN
LYS E:4 E:4 191.0 0.955 H -60.6 -40.8 NA NA NA
5vzw 1 P62837 94.44 5e-101 X-RAY
2017-08-09 LYS A:4 A:4 179.0 0.895 H -60.5 -47.3 123.0 0.615 0.28 C:P36406:0.28
ZN
8.486
HE3
ZN
LYS E:4 B:4 180.0 0.9 H -59.3 -46.5 121.0 0.605 0.295 D:P36406:0.295
ZN
8.608
HE3
ZN
7ahz 2 Q28EY6 94.44 5e-101 X-RAY
2021-01-20 LYS B:4 BBB:4 186.0 0.93 H -68.3 -35.6 NA NA NA
LYS E:4 EEE:4 191.0 0.955 H -66.5 -35.9 NA NA NA
LYS H:4 HHH:4 185.0 0.925 H -66.6 -37.0 NA NA NA
LYS K:4 KKK:4 181.0 0.905 H -65.6 -37.7 NA NA NA
7ai0 2 P62837 94.44 5e-101 X-RAY
2021-01-20 LYS B:4 BBB:4 187.0 0.935 H -66.8 -42.7 NA NA NA
LYS E:4 EEE:4 187.0 0.935 H -64.9 -40.5 NA NA NA
7ai1 2 P62837 94.44 5e-101 X-RAY
2021-01-20 LYS B:4 BBB:4 186.0 0.93 H -64.1 -40.3 NA NA NA
LYS E:4 EEE:4 85.0 NA H -60.6 -42.9 NA NA NA
3zni 3 P62837 94.44 6e-101 X-RAY
2013-07-10 LYS C:3 C:4 187.0 0.935 H -58.6 -37.8 123.0 0.615 0.32 A:Q13191:0.32
ZN
HOH
9.713
3.179
CB
N
ZN
O
LYS G:3 G:4 184.0 0.92 H -72.8 -34.7 NA NA NA
LYS K:3 K:4 85.0 NA H -65.2 -41.9 NA NA NA
LYS O:3 O:4 83.0 NA H -58.9 -42.1 NA NA NA
4v3k 1 P62837 94.44 6e-101 X-RAY
2015-04-08 LYS A:3 A:4 157.0 0.785 H -61.9 -45.8 NA NA NA
LYS D:3 D:4 71.0 NA H -63.5 -41.1 71.0 NA NA CL
HOH
3.867
3.471
N
N
CL
O
6sqo 2 P62837 94.44 6e-101 X-RAY
2020-05-06 LYS B:3 B:4 195.0 0.975 H -60.1 -41.2 138.0 0.69 0.285 A:Q00987:0.285
ZN
CL
HOH
8.919
3.348
2.818
CE
N
O
ZN
CL
O
LYS E:3 E:4 190.0 0.95 H -59.1 -44.6 138.0 0.69 0.26 D:Q00987:0.26
ZN
CL
HOH
9.117
3.383
2.782
CD
N
O
ZN
CL
O
6sqr 2 P62837 94.44 6e-101 X-RAY
2020-05-06 LYS B:3 B:4 183.0 0.915 H -59.8 -46.8 113.0 0.565 0.35 A:Q7YRZ8:0.35
ZN
EDO
HOH
9.495
9.403
3.125
CD
O
N
ZN
C2
O
LYS E:3 E:4 178.0 0.89 H -59.5 -41.2 113.0 0.565 0.325 D:Q7YRZ8:0.325
NO3
ZN
HOH
6.618
9.479
2.588
CD
CD
NZ
O3
ZN
O
LYS H:3 H:4 183.0 0.915 H -60.4 -40.7 122.0 0.61 0.305 G:Q7YRZ8:0.305
ZN
NO3
HOH
9.594
9.072
3.747
CG
O
NZ
ZN
O3
O
LYS K:3 K:4 184.0 0.92 H -64.2 -35.7 81.0 0.405 0.515 B:P62837:0.225
J:Q7YRZ8:0.325
ZN
EDO
HOH
9.766
9.467
3.533
CD
O
NZ
ZN
C2
O
6sqs 2 P62837 94.44 6e-101 X-RAY
2020-05-06 LYS B:3 B:4 182.0 0.91 H -66.6 -40.9 112.0 0.56 0.35 A:Q7YRZ8:0.35
ZN
HOH
9.726
2.900
NZ
O
ZN
O
LYS E:3 E:4 183.0 0.915 H -65.8 -41.4 118.0 0.59 0.325 D:Q7YRZ8:0.325
ZN
HOH
9.840
3.386
CG
N
ZN
O
5edv 2 P62837 94.44 9e-101 X-RAY
2016-01-20 LYS C:6 C:4 186.0 0.93 H -61.6 -41.2 186.0 0.93 0.0
LYS D:6 D:4 144.0 0.72 H -61.9 -41.0 NA NA NA
LYS I:6 I:4 137.0 0.685 H -62.2 -40.8 NA NA NA
4auq 1 P62837 93.75 2e-100 X-RAY
2012-08-15 LYS A:4 A:4 159.0 0.795 H -53.9 -50.0 109.0 0.545 0.25 B:Q96CA5:0.25
HOH
3.903
CB
O
LYS D:4 D:4 159.0 0.795 H -50.7 -49.3 121.0 0.605 0.19 E:Q96CA5:0.19
HOH
3.546
NZ
O
6ttu 6 P62837 93.75 7e-100 EM
2020-02-12 LYS F:4 D:4 84.0 NA H -64.1 -44.9 54.0 NA NA E:P62877:NA
1z2u 1 P35129 90.97 8e-99 X-RAY
2005-03-22 LYS A:7 A:4 146.0 0.73 H -63.2 -41.5 146.0 0.73 0.0 CL
HOH
3.188
2.729
NZ
O
CL
O
2oxq 1 Q6PC58 88.89 8e-98 X-RAY
2008-02-19 LYS A:9 A:4 133.0 0.665 H -62.7 -46.3 111.0 0.555 0.11 C:Q7ZTZ6:0.11
LYS B:9 B:4 149.0 0.745 H -61.8 -41.1 86.0 0.43 0.315 D:Q7ZTZ6:0.315
CL
9.830
NZ
CL
3oj4 1 P51668 86.81 4e-95 X-RAY
2010-12-08 LYS A:10 A:4 149.0 0.745 H -69.4 -47.7 149.0 0.745 0.0
LYS D:10 D:4 145.0 0.725 H -67.9 -48.2 NA NA NA
3ptf 1 P51668 86.81 4e-95 X-RAY
2011-05-11 LYS A:10 A:4 155.0 0.775 H -61.4 -42.0 155.0 0.775 0.0 HOH
7.688
O
O
LYS B:10 B:4 155.0 0.775 H -62.0 -42.6 NA NA NA
2yho 2 P51668 86.81 5e-95 X-RAY
2011-06-29 LYS B:6 B:4 153.0 0.765 H -67.7 -40.4 81.0 0.405 0.36 A:Q8WY64:0.36
ZN
HOH
9.258
2.728
CB
O
ZN
O
LYS D:6 D:4 169.0 0.845 H -64.5 -40.6 NA NA NA
LYS F:6 F:4 160.0 0.8 H -62.1 -38.7 NA NA NA
LYS H:6 H:4 150.0 0.75 H -63.3 -39.3 NA NA NA
6d4p 1 P51668 86.81 5e-95 X-RAY
2019-07-17 LYS A:6 A:4 49.0 NA H -60.7 -38.8 49.0 NA NA HOH
8.624
O
O
4qpl 2 P51668 86.81 6e-95 X-RAY
2014-10-15 LYS B:11 B:4 122.0 0.61 H -66.6 -39.6 64.0 0.32 0.29 A:Q9CZW6:0.29
ZN
HOH
9.853
2.779
CB
O
ZN
O
LYS D:11 D:4 133.0 0.665 H -63.7 -41.3 NA NA NA
6t7f 2 P61077 95.14 6e-95 X-RAY
2020-08-05 LYS B:7 B:4 64.0 NA H -61.2 -36.0 44.0 NA NA A:O75592:NA
HOH
3.888
CA
O
2c4p 1 P51668 86.81 7e-95 X-RAY
2006-11-22 LYS A:22 A:4 125.0 0.625 H -68.1 -32.3 125.0 0.625 0.0 HOH
2.685
NZ
O
LYS B:22 B:4 134.0 0.67 H -79.4 -34.4 NA NA NA
5tut 1 P51668 86.11 1e-93 X-RAY
2017-11-08 LYS A:7 A:4 161.0 0.805 H -65.5 -48.1 161.0 0.805 0.0
6w7z 1 P62837 93.06 2e-93 X-RAY
2020-05-20 LYS A:9 A:4 170.0 0.85 H -63.0 -40.6 165.0 0.825 0.025 B:Q9NVW2:0.025
ZN
HOH
9.894
2.710
CD
O
ZN
O
5d0k 1 P62837 93.06 3e-93 X-RAY
2015-12-09 LYS A:9 A:4 135.0 0.675 H -57.3 -39.8 135.0 0.675 0.0
LYS C:9 D:4 134.0 0.67 H -61.2 -36.7 NA NA NA
LYS E:9 G:4 149.0 0.745 H -61.6 -33.5 NA NA NA
LYS G:9 J:4 131.0 0.655 H -69.4 -31.7 NA NA NA
5ulh 1 P62837 93.06 3e-93 X-RAY
2017-06-07 LYS A:9 A:4 165.0 0.825 H -56.8 -45.0 144.0 0.72 0.105 C:Q6ZSG1:0.105
ZN
HOH
8.446
2.620
NZ
O
ZN
O
5ulk 1 P62837 93.06 3e-93 X-RAY
2017-06-07 LYS A:9 A:4 129.0 0.645 H -58.3 -47.5 125.0 0.625 0.02 C:Q6ZSG1:0.02
ZN
9.466
CE
ZN
4ap4 2 P51668 85.42 6e-93 X-RAY
2012-07-25 LYS B:10 B:4 144.0 0.72 H -66.8 -42.0 86.0 0.43 0.29 A:O88846:0.29
ZN
HOH
9.340
3.541
NZ
CE
ZN
O
LYS D:10 E:4 159.0 0.795 H -67.0 -39.9 156.0 0.78 0.015 A:O88846:0.015
HOH
4.935
CB
O
5fer 2 P51668 85.42 9e-93 X-RAY
2016-05-18 LYS B:7 B:4 150.0 0.75 H -67.8 -37.9 99.0 0.495 0.255 A:Q14258:0.255
LYS E:7 E:4 95.0 0.475 H -64.1 -44.3 95.0 0.475 0.0 HOH
4.137
CB
O
6w9d 1 P62837 92.36 1e-92 X-RAY
2020-05-20 LYS A:4 A:4 177.0 0.885 H -65.4 -32.6 169.0 0.845 0.04 B:Q9NVW2:0.04
LYS D:4 D:4 170.0 0.85 H -66.6 -31.2 NA NA NA
LYS G:4 G:4 159.0 0.795 H -69.5 -35.7 NA NA NA
5d0m 1 P62837 92.36 2e-92 X-RAY
2015-12-09 LYS A:9 A:4 68.0 NA H -62.5 -43.6 68.0 NA NA ZN
HOH
9.539
8.035
CB
N
ZN
O
5ulf 1 P62837 92.36 2e-92 X-RAY
2017-06-07 LYS A:9 A:4 128.0 0.64 H -61.4 -42.1 128.0 0.64 0.0 HOH
2.732
O
O
LYS C:9 C:4 124.0 0.62 H -61.2 -41.8 NA NA NA
4ii2 3 P46595 80.56 3e-87 X-RAY
2013-02-13 LYS C:4 C:4 128.0 0.64 H -71.6 -27.2 25.0 0.125 0.515 A:O94609:0.515
EDO
HOH
7.668
2.842
NZ
NZ
O2
O

AlphaFold DB

Entity Residue Monomer View
ID Entity Uniprot Identity Evalue Name Label Auth ASA rASA SS φ ψ
af-p61077-f1 1 P61077 97.92 5e-105 LYS A:4 A:4 178.0 0.89 H -64.6 -40.6
af-p62837-f1 1 P62837 95.83 2e-103 LYS A:4 A:4 178.0 0.89 H -65.2 -39.3
af-q9y2x8-f1 1 Q9Y2X8 90.28 3e-99 LYS A:4 A:4 169.0 0.845 H -60.7 -38.6
af-p51668-f1 1 P51668 86.81 3e-95 LYS A:4 A:4 168.0 0.84 H -61.0 -38.7